Of course depends on the particulars of the system, but I wager they're talking about static environments, i.e. the background on which characters move, since they're all handcrafted (as opposed to rendered). Flags etc. could be placed as separate objects on top of the background, however, and could then in theory have the same customizability as characters, if such was implemented. Technically there's nothing particularly challenging about allowing a free choice of colour schemes -- as you said, this mechanism is already in place for character armours, so if the devs had the foresight of extending the functionality to other objects as well, it wouldn't even be any great amount of work.